Informatics Publishing Limited

Mohua Chakraborty ¹, S. K. Ghosh ¹, Bishal Dhar ¹, Bijoya Khomdram Devi ¹

Affiliations
1 DNA barcode and Genomics Laboratory, Department of Biotechnology, Assam University, Silchar-788011, Assam, IN

Abstract

Clarias batrachus is a species of freshwater catfish widely used for human consumption. Increasing demand of this species worldwide, coupled with its ability to survive in wide range of environmental conditions, has led to its introduction in many countries. This widespread translocation and distribution of C. batrachus have resulted in the rise of wide variety of haplotypes of this species. Nevertheless, there has been constant decrement in their population density in the last two decades. Thus, to endeavour conservation of the species we employ molecular technique of DNA barcoding in solving the standing problem of crypticism and haplotype sharing of the species. A better knowhow of the genetic makeup of the unique identifier region, that is, the 648 basepair region of COI DNA barcode will help to differentiate among closely related species and identify endemic species. In this study, a comparative analysis of C. batrachus from different regions in India and other parts of world shows presence of distinct haplotypes in different geographical locations. We also present a descriptive study of the various species of Clarias genus that have been barcoded in India till date. Our results also solve the dilemma of considering some species as synonymy of C. batrachus.

Keywords

Clarias batrachus, Cytochrome C Oxidase Subunit I (COI), Genetic Diversity, Kimura's Two Parameter (K2P), Mean Divergence, Neighbour Joining Tree.

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P. Mahadani ¹, M. M. Das ¹, Bishal Dhar ¹, P. R. Ghosh ², S. K. Ghosh ¹

Affiliations
1 DNA barcode and Genomics Laboratory, Department of Biotechnology, Assam University, Silchar-788011, Assam, IN
2 West Bengal University of Animal and Fishery Sciences, Kolkata-700037, IN

Abstract

The plant Anisomeles indica (Lamiaceae) is commonly known as 'Indian Catmint' which is traditionally used as an anticancer and anti-inflammatory and as a source of new anti-metastatic agent for food and pharmaceutical industries. Here, we adopt the plant DNA barcoding technique to develop species level DNA passport for Anisomeles indica based on matK sequence (-800bp) of chloroplast DNA isolated from Anisomeles indica with subsequent amplification and sequencing for species level identification. Our result demonstrated 100% similarity with other Anisomeles indica sequences retrieved from global databases. The phylogeny analysis revealed that Anisomeles indica formed distinctive clusters with its different closely related species assigning correct taxonomic position. We propose that matK gene may be used as DNA passport for medicinal plants.

Keywords

Anisomeles indica, DNA Passport, MatK, Sequence Homology, Species Level.

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Fazlur Rahman Talukdar ¹, Sankar K. Ghosh ¹, Ruhina S. Laskar ¹, Pradosh Mahadani ¹, Mohua Chakraborty ¹, Bishal Dhar ¹, M. Joyraj Bhattacharjee ¹

Affiliations
1 Department of Biotechnology, Assam University, Silchar-788011, Assam, IN

Abstract

DNA markers (barcode) differentiate species based on their nucleotide sequence diversity among various species. In this study we analyzed the rate and pattern of nucleotide substitution and their consequent influence on the amino acid substitution patterns of the sequences used as barcode mitochondrial COI, cyt b and the exon 1 of nuclear IRBP gene for animals from 15 different species of vertebrates. The analysis shows unlike other codon positions, nucleotide substitution at the third codon position does not show strong correlation with the amino acid substitution, for the three gene sequences. Furthermore, COI gene shows a very low percentage of amino acid variability (15.38%) inspite of high percentage of variation in its nucleotide sequence (40.76%) as well as a significantly (p<0.0001) low level of amino acid sequence divergence than the other gene fragments under study. Interestingly among the compared sequences, a significantly conserved amino acid substitution pattern seems to be a unique feature of barcode region of the COI gene making it a more efficient marker for species identification. Hence, it was concluded that the property of species identification of these sequences is based upon the variable nature of third codon position.

Keywords

Species-Specific Marker, DNA Barcoding, Nucleotide Substitution, Codon Positions, Amino Acid Substitution.

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Maloyjo J. Bhattacharjee ¹, Boni A. Laskar ¹, Bishal Dhar ¹, Sankar K. Ghosh ¹

Affiliations
1 Department of Biotechnology, Assam University, Silchar-788011, Assam, IN

Abstract

Cytochrome c oxidase (COI) DNA barcode is considered to be universal species identifier for animals based on many superlative features, but none has considered the pattern of characteristic nucleotide variation for their role if any. In this study, 50 COI barcode sequences of 10 species of catfishes were analyzed in two steps. In the first step, accurate delineation of species was confirmed while the second step involves analysis of the nucleotide variability in terms of transition and transversion at the different taxon levels and their subsequent effect on genetic divergence. The analysis revealed that the individuals within all the species exhibit distinct barcode cluster and a straight forward divergence at the congeneric (17.4% ± 1.8%) and conspecific level (0.7% ± 0.3%) allowing their unambiguous identification. Transition was found to be significantly higher (t= 4.85 - 41.12, p<0.0001) than transversion at all the three taxon levels. However, as transversion showed a significant increase (0.47 ± 0.38, 29.65 ± 5.12 and 34.21 ± 5.50) with the increase in taxon comparison (conspecific, congeneric and intergeneric), transition only showed a significant rise (t= 119.6, p<0.00001) between the conspecific (1.64 ± 0.76) and congeneric level (54.96 ± 6.75) and then transition became saturated at the intergeneric level (54.83 ± 6.68). The study importantly revealed that the genetic divergence between the congeners at the partial fragment of COI was highly correlated (Pearson correlation, R= 0.935, P<0.001) with transversional substitution than with transition (R= 0.334, P<0.05). Hence, although transition is more frequent, still transversional substitution within the COI barcode sequence plays the key role in species delineation.

Keywords

COI, DNA Barcode, Nucleotide Substitution, Transition, Transversion.

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Bijoya Khomdram Devi ¹, Bishal Dhar ¹, Boni Amin Laskar ¹, Sankar Kumar Ghosh ²

Affiliations
1 DNA barcode and Genomics Laboratory, Department of Biotechnology, Assam University, Silchar-788011, Assam, IN
2 Department of Biotechnology, Assam University, Silchar-788011, Assam, IN

Abstract

DNA barcoding is an effective technique of species identification. The large reference library of DNA barcode should be enriched from every region and may be assessed together with morphological taxonomy for species authentication. In this study, a total of 27 fish samples belonging to 21 different species having ornamental relevance were collected and morphologically identified from Manipur, Northeast India. DNA was isolated from muscle tissue of samples and then COI barcode region was amplified using universal fish primers, sequenced and submitted to NCBI (Accession nos. JQ713844 - JQ713860). The sample sequences were identified through similarity search in two databases : GenBank and BOLD. Both the databases revealed definitive identity matches in the range of 98.37% - 100% for 44% of the species. This indicated that the database still lacks reference data of ornamental fishes of Manipur and this study contributed new barcode sequences of ornamental fishes.

Keywords

Ornamental Fish, Manipur, DNA Barcoding, COI, Sequence Homology.

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